Why are we unable to see/perceive atoms on or inside the eye. How do the atoms of the lens not obstruct the view of the pupil? Or what about atoms or cells inside the pupil that are even closer to the RGB cones?
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An atom is an unbelievably small “object”. To even call it one is straining the definition of what an object is.
The first thing to understand is that to “see” something, light must be able to bounce off it and get to your eye and your optic nerve. The wavelength of visible light is about ten thousand times the diameter of an atom, so there’s no way to actually perceive an individual atom- they’re just too small.
When atoms are arranged into molecules, those molecules can then be arranged into material that becomes large enough to interact with light waves in a meaningful way, so light can reflect off it and bounce back to your eye and optic nerve.
Some materials can be transparent to certain wavelengths of light- like glass, or the lens in your eye, so when light at specific frequencies encounters such material, it simply passes through unhindered.
Individual atoms are much smaller than visible light waves. The result is that they be ‘seen’ by visible light, as it mostly just passes around them.
On top of that, many atoms do not absorb light at all. Certainly the ones in the lens and fluid of the eye. Water, for instance. The light does slow down passing through, but it does not get stopped, so it does not create a shadow.
Go to the ocean with a pencil. When a wave comes by hold up the pencil. Did it appreciably alter the wave? Did the wave break in two and go off in different directions? Did the wave stop and reverse its direction when it hit the pencil? Was the water calm and placid behind the pencil?
Now look at a break water. Did this alter the wave appreciably? Did the wave go in two different directions around the break water? Did the breakwater stop the wave? Was the water calm and placid on the shore side of the breakwater?
The atom is like the pencil. It is MUCH smaller than the wavelength and it doesn’t disrupt the light’s wavefront appreciably for you to detect it.
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